| Accession | GMS-97-3
URL copied to the clipboard |
| Title | 4D Genome Analysis Using PHi-C2 |
| Submit date | 2025-05-13 15:08:16 |
| Last update date | 2025-05-13 15:13:43 |
| Contact | Soya SHINKAI soya.shinkai AT riken.jp RIKEN BDR |
| Sharing | |
| Total file size | 812.60 KB |
| Keywords | PHi-C2 Genome DNA Mesoscale MSD analysis Viscoelasticity Rheology |
| Experiment type | PHi-C2 MSD analysis Rheology analysis |
| Summary | Hi-C methods reveal 3D genome features but lack correspondence to dynamic chromatin behavior. PHi-C2, Python software, addresses this gap by transforming Hi-C data into polymer models. After the optimization algorithm, it enables us to calculate 3D conformations and conduct dynamic simulations, providing insights into chromatin dynamics, including the mean-squared displacement and rheological properties. This chapter introduces PHi-C2 usage, offering a tutorial for comprehensive 4D genome analysis. |
| Citation(s) | Shinkai, S., Onami, S. (2025) 4D Genome Analysis Using PHi-C2. In: Nakato, R. (eds) Computational Methods for 3D Genome Analysis. Methods in Molecular Biology 2856, 271–279 https://link.springer.com/protocol/10.1007/978-1-0716-4136-1_16 |
| Organism | Mouse |
| Cell (Tissue) | embryonic stem cell |
| Protocol | |
| Data processing |
| [982] fig3.pdf
A 4D genome analysis of PHi-C2 for mESCs (chr1: 130–135 Mb, 25-kb bins) application/pdf 363.37 KB MD5: b060bef66a4caca3be89341fc99921e6 |
| [983] fig3.png
A 4D genome analysis of PHi-C2 for mESCs (chr1: 130–135 Mb, 25-kb bins) image/png 449.23 KB MD5: cf10ab2bc0bab1608ddc7769785ee5b3 |
